Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010886.1 Kokia drynarioides strain JFW-HI SEQ_125854, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5003
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Found at i:989 original size:17 final size:17
Alignment explanation
Indices: 962--1031 Score: 95
Period size: 17 Copynumber: 4.1 Consensus size: 17
952 TAATTCTAAG
*
962 TTTATAATAAATTTAAA
1 TTTAAAATAAATTTAAA
**
979 TTTCCAATAAATTTAAA
1 TTTAAAATAAATTTAAA
* *
996 TTTAAAATAAACTTAAT
1 TTTAAAATAAATTTAAA
1013 TTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
1030 TT
1 TT
1032 CTGTTGGGCC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:1606 original size:134 final size:134
Alignment explanation
Indices: 1366--1653 Score: 468
Period size: 134 Copynumber: 2.1 Consensus size: 134
1356 ATTCAGTCTT
* *
1366 CTTCTTAGTATCTCATCAAGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTTAGTATCTCATCAAGAAGATGACCACATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* * *
1431 CAAGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
66 CAAGAAAACGAATTTGGTCCACTTCTCAGTATCTCAACAAGAAGCTAACCATTTTATTGCTTCGA
1496 CCTG
131 CCTG
* * * *
1500 CTTCTTAGTATCTCATCAGGAAGATGTCCACCTCACTTGTTTCAATCCGCTTCTTTGTATCTCAT
1 CTTCTTAGTATCTCATCAAGAAGATGACCACATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* *
1565 CAGGAAAACGAATTTGGTCCACTTCTCAGTATCTTAACAAGAAGCTAACCATTTTATTGCTTCGA
66 CAAGAAAACGAATTTGGTCCACTTCTCAGTATCTCAACAAGAAGCTAACCATTTTATTGCTTCGA
1630 CCTG
131 CCTG
*
1634 CTTCTCAGTATCTCATCAAG
1 CTTCTTAGTATCTCATCAAG
1654 CAGCTGAGGT
Statistics
Matches: 141, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 141 1.00
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (134 bp):
CTTCTTAGTATCTCATCAAGAAGATGACCACATCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
CAAGAAAACGAATTTGGTCCACTTCTCAGTATCTCAACAAGAAGCTAACCATTTTATTGCTTCGA
CCTG
Found at i:1874 original size:201 final size:201
Alignment explanation
Indices: 1511--1943 Score: 670
Period size: 201 Copynumber: 2.2 Consensus size: 201
1501 TTCTTAGTAT
* * * *
1511 CTCATCAGGAAGATGTCCACCTCACTTGTTTCAATCCGCTTCTTTGTATCTCATCAGGAAAACGA
1 CTCATCAGGAAGATGTCCGCCTCACTTGTTTCAATCCGCTTCTCTATATCTCATCAAGAAAACGA
*
1576 ATTTGGTCCACTTCTCAGTATCTTAACAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
66 ATTTGGTCCACTTCTCAGTATCTCAACAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
* *
1641 GTATCTCATCAAGCAGCTGAGGTTCAAAGATTTGCTCGCATTGAGCCTTGAGTTGGTATACTTCT
131 GTATCTCATCAAGCAGCTGAGGTTCAAAGATTTGCTCGCATTGAGCCCTGAGTTGGTATACTTCG
1706 CTGTAC
196 CTGTAC
* * *
1712 CTCATCAGGAAAATGTTCGCCTCACTTGTTTCAATCCGCTTCTCTATATCTCATCAAGAAGACGA
1 CTCATCAGGAAGATGTCCGCCTCACTTGTTTCAATCCGCTTCTCTATATCTCATCAAGAAAACGA
* * *
1777 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCC
66 ATTTGGTCCACTTCTCAGTATCTCAACAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
* * * * *
1842 GTATCTCATC-AGGATTCTGGGGTTCGAAGATTTGCTCGCATTGATCCCTGAGTTGGTATACTTC
131 GTATCTCATCAAGCA-GCTGAGGTTCAAAGATTTGCTCGCATTGAGCCCTGAGTTGGTATACTTC
*
1906 GCTGTAT
195 GCTGTAC
*
1913 CTCATCAGGAAGATGACCGCCTCACTTGTTT
1 CTCATCAGGAAGATGTCCGCCTCACTTGTTT
1944 TGGGTAATTG
Statistics
Matches: 209, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
200 3 0.01
201 206 0.99
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (201 bp):
CTCATCAGGAAGATGTCCGCCTCACTTGTTTCAATCCGCTTCTCTATATCTCATCAAGAAAACGA
ATTTGGTCCACTTCTCAGTATCTCAACAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCA
GTATCTCATCAAGCAGCTGAGGTTCAAAGATTTGCTCGCATTGAGCCCTGAGTTGGTATACTTCG
CTGTAC
Done.